5YBA

Dimeric Cyclophilin from T.vaginalis in complex with Myb1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis of interaction between dimeric cyclophilin 1 and Myb1 transcription factor in Trichomonas vaginalis

Martin, T.Lou, Y.C.Chou, C.C.Wei, S.Y.Sadotra, S.Cho, C.C.Lin, M.H.Tai, J.H.Hsu, C.H.Chen, C.

(2018) Sci Rep 8: 5410-5410

  • DOI: 10.1038/s41598-018-23821-5
  • Primary Citation of Related Structures:  
    5YB9, 5YBA

  • PubMed Abstract: 
  • Cyclophilin 1 (TvCyP1), a cyclophilin type peptidyl-prolyl isomerase present in the human parasite Trichomonas vaginalis, interacts with Myb1 and assists in its nuclear translocation. Myb1 regulates the expression of ap65-1 gene that encodes for a disease causing cytoadherence enzyme ...

    Cyclophilin 1 (TvCyP1), a cyclophilin type peptidyl-prolyl isomerase present in the human parasite Trichomonas vaginalis, interacts with Myb1 and assists in its nuclear translocation. Myb1 regulates the expression of ap65-1 gene that encodes for a disease causing cytoadherence enzyme. Here, we determined the crystal structures of TvCyP1 and its complex with the minimum TvCyP1-binding sequence of Myb1 (Myb1 104-111 ), where TvCyP1 formed a homodimer, unlike other single domain cyclophilins. In the complex structure, one Myb1 104-111 peptide was bound to each TvCyP1 protomer, with G106-P107 and Y105 fitting well into the active site and auxiliary S2 pocket, respectively. NMR data further showed that TvCyP1 can catalyze the cis/trans isomerization of P107 in Myb1 104-111 . Interestingly, in the well-folded Myb1 protein (Myb1 35-141 ), the minimum binding sequence adopted a different conformation from that of unstructured Myb1 104-111 peptide, that could make P107 binding to the active site of TvCyP1 difficult. However, NMR studies showed that similar to Myb1 104-111 peptide, Myb1 35-141 also interacted with the active site of TvCyP1 and the dynamics of the Myb1 35-141 residues near P107 was reduced upon interaction. Together, the structure of TvCyP1 and detailed structural insights on TvCyP1-Myb1 interaction provided here could pave the way for newer drugs to treat drug-resistant strains.


    Organizational Affiliation

    Institute of Biomedical Sciences, Academia Sinica, Taipei, 115, Taiwan. bmchinp@ibms.sinica.edu.tw.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Myb1 peptideA [auth B], C [auth D]8Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_473470
UniProt
Find proteins for Q58HP2 (Trichomonas vaginalis)
Explore Q58HP2 
Go to UniProtKB:  Q58HP2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomeraseB [auth A], D [auth C]175Trichomonas vaginalisMutation(s): 0 
Gene Names: TVAG_004440
EC: 5.2.1.8
UniProt
Find proteins for A2DT06 (Trichomonas vaginalis)
Explore A2DT06 
Go to UniProtKB:  A2DT06
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.785α = 90
b = 78.071β = 90
c = 117.708γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-07-18
    Type: Initial release
  • Version 1.1: 2018-08-01
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2018-09-12
    Changes: Data collection, Database references